15-69793977-C-T

Position:

• chr15-69793977-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647319.1(DRAIC):​n.1229+817C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 151,962 control chromosomes in the GnomAD database, including 43,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.75 (43820 hom., cov: 30)
• Consequence: DRAIC ENST00000647319.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

DRAIC (HGNC:27082): (downregulated RNA in cancer, inhibitor of cell invasion and migration)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRAIC	ENST00000647319.1	n.1229+817C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114261 AN: 151844 Hom.: 43806 Cov.: 30

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.756

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.752 AC: 114311 AN: 151962 Hom.: 43820 Cov.: 30 AF XY: 0.746 AC XY: 55432 AN XY: 74274

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.749

Alfa AF: 0.803 Hom.: 56356

Bravo AF: 0.737

Asia WGS AF: 0.529 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.20
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs305039; hg19: chr15-70086316;